SCARA5

scavenger receptor class A member 5, the group of MicroRNA protein coding host genes|Scavenger receptor cysteine rich domain containing|Scavenger receptors

Basic information

Region (hg38): 8:27869883-27992673

Links

ENSG00000168079 ∙ NCBI:286133 ∙ OMIM:611306 ∙ HGNC:28701 ∙ Uniprot:Q6ZMJ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCARA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCARA5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	1	0

Variants in SCARA5

This is a list of pathogenic ClinVar variants found in the SCARA5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-27872011-G-A		not specified	Uncertain significance (Apr 23, 2024)
8-27872050-C-T		not specified	Uncertain significance (Apr 23, 2024)
8-27879695-A-G		not specified	Uncertain significance (Oct 27, 2022)
8-27879718-G-A		not specified	Uncertain significance (Oct 20, 2023)
8-27879749-T-C		not specified	Uncertain significance (May 06, 2024)
8-27879751-G-A		not specified	Uncertain significance (Jun 22, 2024)
8-27904784-C-T		not specified	Uncertain significance (Feb 15, 2023)
8-27907162-A-C		not specified	Uncertain significance (Feb 17, 2023)
8-27907196-C-T		not specified	Uncertain significance (Nov 18, 2023)
8-27907235-C-T		not specified	Uncertain significance (Sep 06, 2022)
8-27907238-C-T		not specified	Uncertain significance (Jul 06, 2021)
8-27909737-G-A		not specified	Uncertain significance (Dec 26, 2023)
8-27921657-A-G		not specified	Uncertain significance (Apr 12, 2023)
8-27921688-C-T		not specified	Uncertain significance (Apr 22, 2022)
8-27921699-C-G		not specified	Uncertain significance (Mar 07, 2024)
8-27921709-G-A		not specified	Uncertain significance (May 31, 2023)
8-27921715-C-T		not specified	Uncertain significance (Dec 19, 2022)
8-27921741-C-T		not specified	Likely benign (Feb 01, 2023)
8-27921813-C-T		not specified	Uncertain significance (Dec 20, 2023)
8-27921868-C-T		not specified	Uncertain significance (Jan 18, 2022)
8-27921885-C-T		not specified	Uncertain significance (Nov 08, 2022)
8-27921920-C-A		not specified	Uncertain significance (Feb 05, 2024)
8-27921921-T-C		not specified	Uncertain significance (Jan 29, 2024)
8-27921934-G-T		not specified	Uncertain significance (Mar 18, 2024)
8-27921969-C-T		not specified	Uncertain significance (Jan 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCARA5	protein_coding	protein_coding	ENST00000354914	8	122846

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000104	0.945	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.382	287	306	0.939	0.0000214	3122
Missense in Polyphen		84	97.454	0.86194		989
Synonymous	1.67	115	140	0.820	0.0000106	1036
Loss of Function	1.79	11	19.5	0.563	0.00000104	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000171	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.0000967
Middle Eastern	0.000171	0.000163
South Asian	0.0000679	0.0000653
Other	0.000178	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ferritin receptor that mediates non-transferrin- dependent delivery of iron. Mediates cellular uptake of ferritin- bound iron by stimulating ferritin endocytosis from the cell surface with consequent iron delivery within the cell. Delivery of iron to cells by ferritin is required for the development of specific cell types, suggesting the existence of cell type- specific mechanisms of iron traffic in organogenesis, which alternatively utilize transferrin or non-transferrin iron delivery pathways. Ferritin mediates iron uptake in capsule cells of the developing kidney. Binds preferrentially ferritin light chain (FTL) compared to heavy chain (FTH1). {ECO:0000255|HAMAP- Rule:MF_03070}.
• Pathway: Vesicle-mediated transport;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.162
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.42

Haploinsufficiency Scores

• pHI: 0.184
• hipred: N
• hipred_score: 0.417
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Scara5
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; immune system phenotype; renal/urinary system phenotype; liver/biliary system phenotype; respiratory system phenotype; reproductive system phenotype

Gene ontology

• Biological process: cellular iron ion homeostasis;endocytosis;receptor-mediated endocytosis;cellular response to heat;iron ion transmembrane transport;protein homotrimerization
• Cellular component: integral component of plasma membrane;cell surface
• Molecular function: scavenger receptor activity;ferritin receptor activity